process {

    withName: LTRHARVEST {
        ext.prefix = { "${meta.id}_ltrharvest" }
    }

    withName: LTRFINDER {
        ext.args = '-harvest_out -size 1000000 -time 300'
    }

    withName: CAT_CAT {
        ext.prefix = { "${meta.id}_ltrharvest_ltrfinder.tabout" }
    }

    withName: UNMASK_IF_ANY {
        ext.args = '-u' // Change lowercase to uppercase
    }
}
